6ZRU

Crystal structure of SARS CoV2 main protease in complex with inhibitor Boceprevir


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6LU7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.75291100 mM MES pH 6.75 5% DMSO (V/V) 16% PEG 6000 (W/V) 300 uM Boceprevir
Crystal Properties
Matthews coefficientSolvent content
2.0239.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.763α = 90
b = 53.535β = 101.52
c = 45.876γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2020-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.033200PETRA III, DESYP11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.148.261000.040.0440.017123.96.815941
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.161000.7020.7580.2840.837

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6LU72.144.961517376699.970.1890.18760.2154RANDOM50.982
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1.660.12-0.4-1.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.866
r_dihedral_angle_3_deg15.073
r_dihedral_angle_4_deg13.524
r_dihedral_angle_1_deg8.117
r_angle_refined_deg1.654
r_angle_other_deg1.325
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.866
r_dihedral_angle_3_deg15.073
r_dihedral_angle_4_deg13.524
r_dihedral_angle_1_deg8.117
r_angle_refined_deg1.654
r_angle_other_deg1.325
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2340
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction